Main Indicators
In order to partition networks into components or clusters, we deploy a community detection technique based on the Lovain Algorithm (Blondel et al., 2008). The Lovain Algorithm is a heuristic method that attempts to optimize the modularity of communities within a network by maximizing within- and minimizing between-community connectivity. We identify the following communities = knowledge bases.
| com | name | dgr_int | dgr |
|---|---|---|---|
| Knowledge Base 21: KB 1 | |||
| 1 | COX J. MANN M. MAXQUANT ENABLES HIGH PEPTIDE IDENTIFICATION RATES INDIVIDUALIZED P.P.B.-RANGE MASS ACCURACIES AND PROTEOME-WIDE PROTEIN QUANTIFICAT… | 9186 | 10106 |
| 1 | COX J. NEUHAUSER N. MICHALSKI A. SCHELTEMA R.A. OLSEN J.V. MANN M. ANDROMEDA: A PEPTIDE SEARCH ENGINE INTEGRATED INTO THE MAXQUANT ENVIRONMENT (2011) | 4417 | 4685 |
| 1 | COX J. HEIN M.Y. LUBER C.A. PARON I. NAGARAJ N. MANN M. ACCURATE PROTEOME-WIDE LABEL-FREE QUANTIFICATION BY DELAYED NORMALIZATION AND MAXIMAL PEPTI… | 3673 | 3940 |
| 1 | TYANOVA S. TEMU T. SINITCYN P. CARLSON A. HEIN M.Y. GEIGER T. MANN M. COX J. THE PERSEUS COMPUTATIONAL PLATFORM FOR COMPREHENSIVE ANALYSIS OF (PROTE) | 3152 | 3449 |
| 1 | RAPPSILBER J. MANN M. ISHIHAMA Y. PROTOCOL FOR MICRO-PURIFICATION ENRICHMENT PRE-FRACTIONATION AND STORAGE OF PEPTIDES FOR PROTEOMICS USING STAGETI… | 2937 | 3180 |
| 1 | COX J. ANDROMEDA: A PEPTIDE SEARCH ENGINE INTEGRATED INTO THE MAXQUANT ENVIRONMENT (2011) | 1270 | 1379 |
| 1 | TYANOVA S. THE PERSEUS COMPUTATIONAL PLATFORM FOR COMPREHENSIVE ANALYSIS OF (PROTE) | 1245 | 1469 |
| 1 | COX J. ACCURATE PROTEOME-WIDE LABEL-FREE QUANTIFICATION BY DELAYED NORMALIZATION AND MAXIMAL PEPTIDE RATIO EXTRACTION TERMED MAXLFQ (2014) | 990 | 1112 |
| 1 | KULAK N.A. PICHLER G. PARON I. NAGARAJ N. MANN M. MINIMAL ENCAPSULATED PROTEOMIC-SAMPLE PROCESSING APPLIED TO COPY-NUMBER ESTIMATION IN EUKARYOTIC … | 681 | 704 |
| 1 | TYANOVA S. TEMU T. COX J. THE MAXQUANT COMPUTATIONAL PLATFORM FOR MASS SPECTROMETRY-BASED SHOTGUN PROTEOMICS (2016) | 649 | 689 |
| Knowledge Base 22: KB 2 | |||
| 2 | BRENNAN C.W. THE SOMATIC GENOMIC LANDSCAPE OF GLIOBLASTOMA (2013) | 1838 | 2007 |
| 2 | LOVE M.I. HUBER W. ANDERS S. MODERATED ESTIMATION OF FOLD CHANGE AND DISPERSION FOR RNA-SEQ DATA WITH DESEQ2 (2014) | 1557 | 2607 |
| 2 | PATEL A.P. SINGLE-CELL RNA-SEQ HIGHLIGHTS INTRATUMORAL HETEROGENEITY IN PRIMARY GLIOBLASTOMA (2014) | 1360 | 1479 |
| 2 | VERHAAK R.G. INTEGRATED GENOMIC ANALYSIS IDENTIFIES CLINICALLY RELEVANT SUBTYPES OF GLIOBLASTOMA CHARACTERIZED BY ABNORMALITIES IN PDGFRA IDH1 EGFR… | 1295 | 1455 |
| 2 | CECCARELLI M. MOLECULAR PROFILING REVEALS BIOLOGICALLY DISCRETE SUBSETS AND PATHWAYS OF PROGRESSION IN DIFFUSE GLIOMA (2016) | 1241 | 1319 |
| 2 | SUBRAMANIAN A. GENE SET ENRICHMENT ANALYSIS: A KNOWLEDGE-BASED APPROACH FOR INTERPRETING GENOME-WIDE EXPRESSION PROFILES (2005) | 1163 | 1411 |
| 2 | DOBIN A. STAR: ULTRAFAST UNIVERSAL RNA-SEQ ALIGNER (2013) | 1136 | 1257 |
| 2 | BUTLER A. HOFFMAN P. SMIBERT P. PAPALEXI E. SATIJA R. INTEGRATING SINGLE-CELL TRANSCRIPTOMIC DATA ACROSS DIFFERENT CONDITIONS TECHNOLOGIES AND SPEC… | 1083 | 1285 |
| 2 | LI H. DURBIN R. FAST AND ACCURATE SHORT READ ALIGNMENT WITH BURROWS-WHEELER TRANSFORM (2009) | 1020 | 1353 |
| 2 | LI H. THE SEQUENCE ALIGNMENT/MAP FORMAT AND SAMTOOLS (2009) | 946 | 985 |
| Knowledge Base 23: KB 3 | |||
| 3 | LOUIS D.N. PERRY A. REIFENBERGER G. VON DEIMLING A. FIGARELLA-BRANGER D. CAVENEE W.K. THE 2016 WORLD HEALTH ORGANIZATION CLASSIFICATION OF TUMORS O… | 2265 | 2513 |
| 3 | YAN H. PARSONS D.W. JIN G. MCLENDON R. RASHEED B.A. YUAN W. IDH1 AND IDH2 MUTATIONS IN GLIOMAS (2009) | 2190 | 2380 |
| 3 | VERHAAK R.G. HOADLEY K.A. PURDOM E. WANG V. QI Y. WILKERSON M.D. INTEGRATED GENOMIC ANALYSIS IDENTIFIES CLINICALLY RELEVANT SUBTYPES OF GLIOBLASTOM… | 2037 | 2231 |
| 3 | STUPP R. MASON W.P. VAN DEN BENT M.J. WELLER M. FISHER B. TAPHOORN M.J. RADIOTHERAPY PLUS CONCOMITANT AND ADJUVANT TEMOZOLOMIDE FOR GLIOBLASTOMA (2… | 2001 | 2143 |
| 3 | COMPREHENSIVE GENOMIC CHARACTERIZATION DEFINES HUMAN GLIOBLASTOMA GENES AND CORE PATHWAYS (2008) | 1722 | 4734 |
| 3 | BRENNAN C.W. VERHAAK R.G. MCKENNA A. CAMPOS B. NOUSHMEHR H. SALAMA S.R. THE SOMATIC GENOMIC LANDSCAPE OF GLIOBLASTOMA (2013) | 1575 | 1685 |
| 3 | CECCARELLI M. BARTHEL F.P. MALTA T.M. SABEDOT T.S. SALAMA S.R. MURRAY B.A. MOLECULAR PROFILING REVEALS BIOLOGICALLY DISCRETE SUBSETS AND PATHWAYS O… | 1329 | 1488 |
| 3 | PARSONS D.W. JONES S. ZHANG X. LIN J.C. LEARY R.J. ANGENENDT P. AN INTEGRATED GENOMIC ANALYSIS OF HUMAN GLIOBLASTOMA MULTIFORME (2008) | 1251 | 1309 |
| 3 | DANG L. WHITE D.W. GROSS S. BENNETT B.D. BITTINGER M.A. DRIGGERS E.M. CANCER-ASSOCIATED IDH1 MUTATIONS PRODUCE 2-HYDROXYGLUTARATE (2009) | 1157 | 1214 |
| 3 | ECKEL-PASSOW J.E. LACHANCE D.H. MOLINARO A.M. WALSH K.M. DECKER P.A. SICOTTE H. GLIOMA GROUPS BASED ON 1P/19Q IDH AND TERT PROMOTER MUTATIONS IN TU… | 972 | 1031 |
| Knowledge Base 24: KB 4 | |||
| 4 | LOUIS D.N. PERRY A. REIFENBERGER G. VON DEIMLING A. FIGARELLA-BRANGER D. CAVENEE W.K. OHGAKI H. ELLISON D.W. THE 2016 WORLD HEALTH ORGANIZATION CLA… | 2495 | 3091 |
| 4 | VERHAAK R.G. HOADLEY K.A. PURDOM E. WANG V. QI Y. WILKERSON M.D. MILLER C.R. MESIROV J.P. INTEGRATED GENOMIC ANALYSIS IDENTIFIES CLINICALLY RELEVAN… | 1521 | 1754 |
| 4 | YAN H. PARSONS D.W. JIN G. MCLENDON R. RASHEED B.A. YUAN W. KOS I. RIGGINS G.J. IDH1 AND IDH2 MUTATIONS IN GLIOMAS (2009) | 1259 | 1418 |
| 4 | BRENNAN C.W. VERHAAK R.G. MCKENNA A. CAMPOS B. NOUSHMEHR H. SALAMA S.R. ZHENG S. BERMAN S.H. THE SOMATIC GENOMIC LANDSCAPE OF GLIOBLASTOMA (2013) | 1137 | 1406 |
| 4 | PATEL A.P. TIROSH I. TROMBETTA J.J. SHALEK A.K. GILLESPIE S.M. WAKIMOTO H. CAHILL D.P. MARTUZA R.L. SINGLE-CELL RNA-SEQ HIGHLIGHTS INTRATUMORAL HET… | 1015 | 1388 |
| 4 | DANG L. WHITE D.W. GROSS S. BENNETT B.D. BITTINGER M.A. DRIGGERS E.M. FANTIN V.R. KEENAN M.C. CANCER-ASSOCIATED IDH1 MUTATIONS PRODUCE 2-HYDROXYGLU… | 845 | 917 |
| 4 | PARSONS D.W. JONES S. ZHANG X. LIN J.C. LEARY R.J. ANGENENDT P. MANKOO P. GALLIA G.L. AN INTEGRATED GENOMIC ANALYSIS OF HUMAN GLIOBLASTOMA MULTIFOR… | 839 | 943 |
| 4 | LOUIS D.N. OHGAKI H. WIESTLER O.D. CAVENEE W.K. BURGER P.C. JOUVET A. SCHEITHAUER B.W. KLEIHUES P. THE 2007 WHO CLASSIFICATION OF TUMOURS OF THE CE… | 831 | 997 |
| 4 | YAN H. PARSONS D.W. JIN G. MCLENDON R. RASHEED B.A. YUAN W. KOS I. BIGNER D.D. IDH1 AND IDH2 MUTATIONS IN GLIOMAS (2009) | 821 | 937 |
| 4 | STUPP R. MASON W.P. VAN DEN BENT M.J. WELLER M. FISHER B. TAPHOORN M.J. BELANGER K. BOGDAHN U. RADIOTHERAPY PLUS CONCOMITANT AND ADJUVANT TEMOZOLOM… | 747 | 928 |
| Knowledge Base 25: KB 5 | |||
| 5 | WHITE E. DECONVOLUTING THE CONTEXT-DEPENDENT ROLE FOR AUTOPHAGY IN CANCER (2012) | 2010 | 2026 |
| 5 | LEVY J.M.M. TOWERS C.G. THORBURN A. TARGETING AUTOPHAGY IN CANCER (2017) | 1844 | 1881 |
| 5 | MATHEW R. KARANTZA-WADSWORTH V. WHITE E. ROLE OF AUTOPHAGY IN CANCER (2007) | 1069 | 1075 |
| 5 | WHITE E. THE ROLE FOR AUTOPHAGY IN CANCER (2015) | 1015 | 1048 |
| 5 | MIZUSHIMA N. YOSHIMORI T. LEVINE B. METHODS IN MAMMALIAN AUTOPHAGY RESEARCH (2010) | 942 | 950 |
| 5 | LEVINE B. KROEMER G. AUTOPHAGY IN THE PATHOGENESIS OF DISEASE (2008) | 898 | 921 |
| 5 | KIMMELMAN A.C. WHITE E. AUTOPHAGY AND TUMOR METABOLISM (2017) | 751 | 769 |
| 5 | MIZUSHIMA N. KOMATSU M. AUTOPHAGY: RENOVATION OF CELLS AND TISSUES (2011) | 698 | 707 |
| 5 | CHUDE C.I. AMARAVADI R.K. TARGETING AUTOPHAGY IN CANCER: UPDATE ON CLINICAL TRIALS AND NOVEL INHIBITORS (2017) | 672 | 675 |
| 5 | MIZUSHIMA N. LEVINE B. CUERVO A.M. KLIONSKY D.J. AUTOPHAGY FIGHTS DISEASE THROUGH CELLULAR SELF-DIGESTION (2008) | 670 | 676 |
| Knowledge Base 26: KB 6 | |||
| 6 | VIVIER E. TOMASELLO E. BARATIN M. WALZER T. UGOLINI S. FUNCTIONS OF NATURAL KILLER CELLS (2008) | 1855 | 1877 |
| 6 | LONG E.O. KIM H.S. LIU D. PETERSON M.E. RAJAGOPALAN S. CONTROLLING NATURAL KILLER CELL RESPONSES: INTEGRATION OF SIGNALS FOR ACTIVATION AND INHIBIT… | 1254 | 1260 |
| 6 | GUILLEREY C. HUNTINGTON N.D. SMYTH M.J. TARGETING NATURAL KILLER CELLS IN CANCER IMMUNOTHERAPY (2016) | 1243 | 1298 |
| 6 | ALTER G. MALENFANT J.M. ALTFELD M. CD107A AS A FUNCTIONAL MARKER FOR THE IDENTIFICATION OF NATURAL KILLER CELL ACTIVITY (2004) | 900 | 918 |
| 6 | GONG J.H. MAKI G. KLINGEMANN H.G. CHARACTERIZATION OF A HUMAN CELL LINE (NK-92) | 630 | 630 |
| 6 | MILLER J.S. SOIGNIER Y. PANOSKALTSIS-MORTARI A. MCNEARNEY S.A. YUN G.H. FAUTSCH S.K. SUCCESSFUL ADOPTIVE TRANSFER AND IN VIVO EXPANSION OF HUMAN HA… | 588 | 588 |
| 6 | COOPER M.A. FEHNIGER T.A. CALIGIURI M.A. THE BIOLOGY OF HUMAN NATURAL KILLER-CELL SUBSETS (2001) | 573 | 573 |
| 6 | LANIER L.L. NK CELL RECOGNITION (2005) | 546 | 550 |
| 6 | VIVIER E. UGOLINI S. BLAISE D. CHABANNON C. BROSSAY L. TARGETING NATURAL KILLER CELLS AND NATURAL KILLER T CELLS IN CANCER (2012) | 529 | 535 |
| 6 | ORANGE J.S. FORMATION AND FUNCTION OF THE LYTIC NK-CELL IMMUNOLOGICAL SYNAPSE (2008) | 529 | 529 |
| Knowledge Base 27: KB 7 | |||
| 7 | LOUIS D.N. PERRY A. REIFENBERGER G. THE 2016 WORLD HEALTH ORGANIZATION CLASSIFICATION OF TUMORS OF THE CENTRAL NERVOUS SYSTEM: A SUMMARY (2016) | 3490 | 3711 |
| 7 | YAN H. PARSONS D.W. JIN G. IDH1 AND IDH2 MUTATIONS IN GLIOMAS (2009) | 3405 | 3621 |
| 7 | PARSONS D.W. JONES S. ZHANG X. AN INTEGRATED GENOMIC ANALYSIS OF HUMAN GLIOBLASTOMA MULTIFORME (2008) | 1996 | 2142 |
| 7 | STUPP R. MASON W.P. VAN DEN BENT M.J. RADIOTHERAPY PLUS CONCOMITANT AND ADJUVANT TEMOZOLOMIDE FOR GLIOBLASTOMA (2005) | 1906 | 2100 |
| 7 | ECKEL-PASSOW J.E. LACHANCE D.H. MOLINARO A.M. GLIOMA GROUPS BASED ON 1P/19Q IDH AND TERT PROMOTER MUTATIONS IN TUMORS (2015) | 1569 | 1658 |
| 7 | DANG L. WHITE D.W. GROSS S. CANCER-ASSOCIATED IDH1 MUTATIONS PRODUCE 2-HYDROXYGLUTARATE (2009) | 1501 | 1592 |
| 7 | BRENNAN C.W. VERHAAK R.G. MCKENNA A. THE SOMATIC GENOMIC LANDSCAPE OF GLIOBLASTOMA (2013) | 1387 | 1545 |
| 7 | VERHAAK R.G. HOADLEY K.A. PURDOM E. INTEGRATED GENOMIC ANALYSIS IDENTIFIES CLINICALLY RELEVANT SUBTYPES OF GLIOBLASTOMA CHARACTERIZED BY ABNORMALIT… | 1195 | 1347 |
| 7 | CECCARELLI M. BARTHEL F.P. MALTA T.M. MOLECULAR PROFILING REVEALS BIOLOGICALLY DISCRETE SUBSETS AND PATHWAYS OF PROGRESSION IN DIFFUSE GLIOMA (2016) | 997 | 1085 |
| 7 | HEGI M.E. DISERENS A.C. GORLIA T. MGMT GENE SILENCING AND BENEFIT FROM TEMOZOLOMIDE IN GLIOBLASTOMA (2005) | 965 | 1014 |